Sequence specifist in protein nuclies acid interaction

Abstract

The interaction specificities of various dipeptides, NH –CH –CO–NH–CH(R)–COO ; (R = H, Leu, Tyr, Ser, Asp, Met, Lys, His) with various mononucleotides have been determined from measurements of nucleotide induced changes in PMR spectra of the dipeptide and from the model building studies. Possible types of noncovalent interactions in these complexes giving rise to the “base specificity” are identified. Finally, some experimental evidence in support of these models has been collected. The apparent binding specificity of mononucleotide and dinucleotide to poly L lysine in all three conformations ( , and random coil) is determined by both K and parameters. In addition to electrostatic interaction, other noncovalent interactions may contribute towards the K value. The relative magnitudes of K and at three different conformations of polylysine indicate that ligand induced conformational transition from coil to helix is not energetically favourable. The interaction specificity of dipeptide (Gly X where X = Gly or Tyr) towards polycytidylic acid follows the same order as that of the affinity of the dipeptides towards the 3 CMP as determined from PMR spectroscopic study. The complex is stabilised by H···O=C bond formation similar to that in helix conformation.